LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
variable	sname index adamantane_ionized

units 		electron
newton		on
boundary        f f f

atom_style	electron

read_data  	data.${sname}
read_data  	data.adamantane_ionized
Reading data file ...
  orthogonal box = (-50 -50 -50) to (50 50 50)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  101 atoms
  read_data CPU = 0.001 seconds

pair_style      eff/cut 100.0
pair_coeff 	* *

comm_modify	vel yes

compute		effTemp all temp/eff

thermo		1000
thermo_style	custom step pe temp etotal press
thermo_modify	temp effTemp

# Minimization
min_style       cg
dump            1 all xyz 500 ${sname}.min.xyz
dump            1 all xyz 500 adamantane_ionized.min.xyz
compute         1 all property/atom spin eradius erforce
dump            2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump            2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
min_modify	line quadratic
minimize        0.0 1.0e-5 10000 100000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- EFF package: doi:10.1002/jcc.21637

@Article{Jaramillo-Botero11,
 author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
 title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
 journal = {J.~Comp.\ Chem.},
 year =    2011,
 volume =  32,
 number =  3,
 pages =   {497--512}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 102
  ghost atom cutoff = 102
  binsize = 51, bins = 2 2 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair eff/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.253 | 5.253 | 5.253 Mbytes
   Step         PotEng          Temp          TotEng         Press     
         0  -320.50186      0             -320.50186     -45590269     
       493  -324.31743      0             -324.31743      20971271     
Loop time of 0.883439 on 4 procs for 493 steps with 101 atoms

99.8% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
     -320.501859657306  -324.317430790588  -324.317430790588
  Force two-norm initial, final = 2.8135352 1.2148731
  Force max component initial, final = 1.7194878 1.1232786
  Final line search alpha, max atom move = 4.245048e-09 4.7683716e-09
  Iterations, force evaluations = 493 3804

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.24614    | 0.45831    | 0.84299    |  34.7 | 51.88
Neigh   | 1.1159e-05 | 1.2751e-05 | 1.5479e-05 |   0.0 |  0.00
Comm    | 0.019423   | 0.40607    | 0.62032    |  37.1 | 45.97
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.01905    |            |       |  2.16

Nlocal:          25.25 ave          30 max          17 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost:          75.75 ave          84 max          71 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs:         1262.5 ave        2394 max         663 min
Histogram: 2 0 0 1 0 0 0 0 0 1

Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 1
Dangerous builds = 0

undump		1
undump		2

#restart		timestep

# set velocities for nve
#velocity	all create 300.0 4928459 dist uniform

# NVE
timestep	0.0001

fix		1 all nve/eff
dump            1 all xyz 1000 ${sname}.nve.xyz
dump            1 all xyz 1000 adamantane_ionized.nve.xyz
dump            2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump            2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
#restart		1000 ${sname}.nve.restart1 ${sname}.nve.restart2

run		200000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.128 | 4.128 | 4.128 Mbytes
   Step         PotEng          Temp          TotEng         Press     
       493  -324.31743      0             -324.31743      20971271     
      1000  -324.2963       3994.2535     -323.82196      29875505     
      2000  -324.14448      2715.8412     -323.82196      24005899     
      3000  -323.9446       1032.7299     -323.82196      16224812     
      4000  -323.83425      103.47941     -323.82196      11886177     
      5000  -323.87559      451.59681     -323.82196      13395168     
      6000  -324.05446      1957.8271     -323.82196      20034811     
      7000  -324.24814      3588.7467     -323.82196      28092249     
      8000  -324.3149       4150.7958     -323.82197      31632418     
      9000  -324.25366      3635.1689     -323.82196      27760974     
     10000  -324.05069      1926.0777     -323.82196      19436396     
     11000  -323.88484      529.46541     -323.82196      13264080     
     12000  -323.86286      344.37477     -323.82196      12741952     
     13000  -324.00393      1532.3029     -323.82196      17720089     
     14000  -324.20987      3266.4109     -323.82196      25528615     
     15000  -324.34308      4388.1934     -323.82196      30700580     
     16000  -324.30475      4065.4216     -323.82196      29168176     
     17000  -324.12375      2541.2612     -323.82196      21928164     
     18000  -323.93619      961.92262     -323.82196      14363951     
     19000  -323.87105      413.39974     -323.82196      11446320     
     20000  -323.9713       1257.5055     -323.82196      15118972     
     21000  -324.16564      2894.0212     -323.82196      22749979     
     22000  -324.32073      4199.9228     -323.82196      29044099     
     23000  -324.34614      4413.8921     -323.82196      29514541     
     24000  -324.20431      3219.6717     -323.82196      23595226     
     25000  -324.01211      1601.1964     -323.82196      15812197     
     26000  -323.90577      705.76969     -323.82196      11992491     
     27000  -323.95668      1134.4631     -323.82196      14679820     
     28000  -324.12645      2564.0146     -323.82196      21299092     
     29000  -324.29158      3954.5234     -323.82196      28120074     
     30000  -324.32731      4255.3405     -323.82196      31311574     
     31000  -324.27771      3837.6901     -323.82196      28270491     
     32000  -324.09259      2278.8862     -323.82196      21338356     
     33000  -323.95465      1117.2898     -323.82196      15833338     
     34000  -323.95469      1117.6477     -323.82196      16034624     
     35000  -324.08796      2239.9037     -323.82196      22076527     
     36000  -324.26866      3761.5323     -323.82196      29147703     
     37000  -324.3502       4448.1533     -323.82196      33380564     
     38000  -324.29459      3979.8076     -323.82196      31533851     
     39000  -324.1694       2925.6774     -323.82196      25161011     
     40000  -324.01365      1614.1815     -323.82196      19145060     
     41000  -323.97015      1247.8234     -323.82196      16994462     
     42000  -324.04755      1899.62       -323.82196      19654332     
     43000  -324.22071      3357.7354     -323.82196      25666317     
     44000  -324.35528      4490.9023     -323.82196      30318540     
     45000  -324.35807      4514.3651     -323.82196      30645986     
     46000  -324.24462      3559.0921     -323.82196      25690532     
     47000  -324.09319      2283.909      -323.82196      18529309     
     48000  -324.00266      1521.597      -323.82196      14177383     
     49000  -324.04261      1858.0104     -323.82196      15780869     
     50000  -324.19619      3151.2862     -323.82196      21070555     
     51000  -324.32727      4255.0227     -323.82196      26451705     
     52000  -324.3917       4797.6094     -323.82196      28066000     
     53000  -324.30169      4039.6086     -323.82196      24214730     
     54000  -324.14884      2752.5491     -323.82196      17848175     
     55000  -324.02946      1747.258      -323.82196      13686029     
     56000  -324.05031      1922.825      -323.82196      14113758     
     57000  -324.16944      2925.9624     -323.82196      18723794     
     58000  -324.30745      4088.1772     -323.82196      24387592     
     59000  -324.36463      4569.6324     -323.82196      27059420     
     60000  -324.32147      4206.1707     -323.82196      25012812     
     61000  -324.18133      3026.1579     -323.82196      19500659     
     62000  -324.07027      2090.9001     -323.82196      14626096     
     63000  -324.04536      1881.129      -323.82196      13606034     
     64000  -324.14417      2713.2333     -323.82196      17524492     
     65000  -324.28817      3925.7771     -323.82196      23261363     
     66000  -324.37816      4683.5409     -323.82196      26852878     
     67000  -324.34311      4388.4452     -323.82196      25854003     
     68000  -324.24346      3549.2763     -323.82196      20818195     
     69000  -324.1067       2397.6992     -323.82196      15550338     
     70000  -324.05471      1959.908      -323.82196      13178617     
     71000  -324.12382      2541.8769     -323.82196      15655087     
     72000  -324.25986      3687.3615     -323.82196      20831733     
     73000  -324.37345      4643.9165     -323.82196      25082640     
     74000  -324.38407      4733.3013     -323.82196      25377064     
     75000  -324.28752      3920.3485     -323.82196      21185087     
     76000  -324.14479      2718.409      -323.82196      15093238     
     77000  -324.06273      2027.4447     -323.82196      11357895     
     78000  -324.1027       2363.9918     -323.82196      12682184     
     79000  -324.24431      3556.4784     -323.82196      17923460     
     80000  -324.37329      4642.461      -323.82197      22977159     
     81000  -324.40875      4941.1418     -323.82196      24175202     
     82000  -324.33677      4334.993      -323.82196      20418362     
     83000  -324.18471      3054.6117     -323.82196      14173787     
     84000  -324.08262      2194.902      -323.82196      10107358     
     85000  -324.07536      2133.7765     -323.82196      9748952.1    
     86000  -324.18707      3074.432      -323.82196      13462472     
     87000  -324.32091      4201.5211     -323.82196      19096674     
     88000  -324.44557      5251.2038     -323.82196      22573960     
     89000  -324.39988      4866.4678     -323.82196      21348490     
     90000  -324.25685      3662.0864     -323.82196      15903121     
     91000  -324.0755       2135.0001     -323.82196      10233161     
     92000  -324.06354      2034.2765     -323.82196      7509452      
     93000  -324.15185      2777.9236     -323.82196      9750370.3    
     94000  -324.30478      4065.6146     -323.82196      15561885     
     95000  -324.42696      5094.5186     -323.82196      20667693     
     96000  -324.44094      5212.1846     -323.82196      21153174     
     97000  -324.33283      4301.8232     -323.82196      16435314     
     98000  -324.1883       3084.8099     -323.82196      10336860     
     99000  -324.09656      2312.304      -323.82196      6808669.9    
    100000  -324.13298      2619.0245     -323.82196      7675912.4    
    101000  -324.25984      3687.2237     -323.82196      11868042     
    102000  -324.40322      4894.6055     -323.82196      17007266     
    103000  -324.44333      5232.3546     -323.82196      19025190     
    104000  -324.39727      4844.4421     -323.82196      15980570     
    105000  -324.25         3604.3886     -323.82196      9668044.1    
    106000  -324.08507      2215.5839     -323.82196      4405958.8    
    107000  -324.11835      2495.8211     -323.82196      3436936.2    
    108000  -324.21008      3268.2404     -323.82196      6028268.3    
    109000  -324.34118      4372.1743     -323.82196      10939013     
    110000  -324.40282      4891.1987     -323.82196      14333667     
    111000  -324.45353      5318.1927     -323.82196      13380345     
    112000  -324.33795      4344.9374     -323.82196      7923709.9    
    113000  -324.19654      3154.2192     -323.82196      1970263.7    
    114000  -324.12867      2582.7343     -323.82196     -1481413.1    
    115000  -324.17132      2941.8126     -323.82196     -290956.43    
    116000  -324.33613      4329.6247     -323.82196      5245770.9    
    117000  -324.41548      4997.8222     -323.82196      10354303     
    118000  -324.48518      5584.7558     -323.82196      11795673     
    119000  -324.41046      4955.5092     -323.82196      8031391.3    
    120000  -324.24749      3583.2536     -323.82196      1845177.6    
    121000  -324.14124      2688.5331     -323.82196     -2784584.1    
    122000  -324.14467      2717.4458     -323.82196     -2261498.4    
    123000  -324.28472      3896.7771     -323.82196      3080452.1    
    124000  -324.43687      5177.9121     -323.82196      9819540.9    
    125000  -324.51452      5831.8132     -323.82196      13180239     
    126000  -324.47691      5515.0823     -323.82196      11018721     
    127000  -324.31812      4178.0163     -323.82196      4976672.9    
    128000  -324.16884      2920.9366     -323.82196     -186371.44    
    129000  -324.13025      2596.0395     -323.82196     -1883126.3    
    130000  -324.22275      3374.922      -323.82196      1526423.1    
    131000  -324.41343      4980.5335     -323.82196      8415685      
    132000  -324.45089      5296.046      -323.82196      13250300     
    133000  -324.51148      5806.2229     -323.82196      12827560     
    134000  -324.39463      4822.239      -323.82196      7049805.8    
    135000  -324.20254      3204.6979     -323.82196     -187723.51    
    136000  -324.1379       2660.4388     -323.82196     -3970679.9    
    137000  -324.18473      3054.7443     -323.82196     -2351010.9    
    138000  -324.35172      4460.9406     -323.82196      3024494.5    
    139000  -324.48743      5603.6722     -323.82196      8652609.2    
    140000  -324.53668      6018.4343     -323.82196      9612584.9    
    141000  -324.43638      5173.8016     -323.82196      4805500.8    
    142000  -324.28353      3886.746      -323.82196     -2740880.4    
    143000  -324.14169      2692.2995     -323.82196     -8310197.6    
    144000  -324.13063      2599.1788     -323.82196     -9603391.1    
    145000  -324.27459      3811.4423     -323.82196     -5690559.8    
    146000  -324.4342       5155.4519     -323.82196      431484.28    
    147000  -324.55834      6200.7798     -323.82196      4166801.6    
    148000  -324.51567      5841.5105     -323.82196      2299540.9    
    149000  -324.34424      4397.967      -323.82196     -4487220.6    
    150000  -324.20348      3212.6032     -323.82196     -10852097     
    151000  -324.13211      2611.6979     -323.82196     -12942852     
    152000  -324.20634      3236.7635     -323.82196     -10732036     
    153000  -324.35827      4516.0788     -323.82196     -4665668.3    
    154000  -324.5074       5771.8121     -323.82196      1703175.2    
    155000  -324.51881      5867.9505     -323.82196      2959605.5    
    156000  -324.44762      5268.4581     -323.82196     -1706620      
    157000  -324.25179      3619.4025     -323.82196     -8511782.3    
    158000  -324.13478      2634.1695     -323.82196     -11767435     
    159000  -324.17085      2937.9043     -323.82196     -10356431     
    160000  -324.28946      3936.6179     -323.82196     -5252437.9    
    161000  -324.47596      5507.0864     -323.82196      1737812.2    
    162000  -324.52686      5935.7476     -323.82196      5782720.9    
    163000  -324.5121       5811.4236     -323.82196      4273238.8    
    164000  -324.35265      4468.7315     -323.82196     -1590319.8    
    165000  -324.19582      3148.1193     -323.82196     -6770200.2    
    166000  -324.15306      2788.0507     -323.82196     -8385908.5    
    167000  -324.24186      3535.8588     -323.82196     -4776412.5    
    168000  -324.4          4867.4913     -323.82196      2207883.7    
    169000  -324.52732      5939.6216     -323.82196      7770368.9    
    170000  -324.53787      6028.4604     -323.82196      8163057.7    
    171000  -324.42167      5049.9129     -323.82196      2893037      
    172000  -324.25784      3670.3642     -323.82196     -4020286      
    173000  -324.16815      2915.1362     -323.82196     -7461767.8    
    174000  -324.21774      3332.737      -323.82196     -5214520.3    
    175000  -324.37502      4657.1185     -323.82196     -81968.156    
    176000  -324.5128       5817.2882     -323.82196      5130806.8    
    177000  -324.4983       5695.2281     -323.82196      6394017.7    
    178000  -324.47309      5482.9629     -323.82196      2466372.3    
    179000  -324.31526      4153.8777     -323.82196     -4378953.5    
    180000  -324.2046       3222.0434     -323.82196     -9221400.9    
    181000  -324.21978      3349.8648     -323.82196     -9338327.2    
    182000  -324.33867      4351.0162     -323.82196     -5586765.2    
    183000  -324.44483      5244.9523     -323.82196     -706564.21    
    184000  -324.54787      6112.6128     -323.82196      1971109.1    
    185000  -324.49436      5662.0508     -323.82196     -1239.0449    
    186000  -324.38425      4734.8404     -323.82196     -5595239.9    
    187000  -324.25734      3666.1954     -323.82196     -10793981     
    188000  -324.21303      3293.0496     -323.82196     -11574584     
    189000  -324.28662      3912.7067     -323.82196     -8579023.4    
    190000  -324.4316       5133.5815     -323.82196     -2888022.8    
    191000  -324.51735      5855.6722     -323.82196      1558206.4    
    192000  -324.55207      6147.9783     -323.82196      1897782.9    
    193000  -324.43491      5161.4381     -323.82196     -1998628.2    
    194000  -324.28751      3920.2514     -323.82196     -6841627.4    
    195000  -324.24114      3529.7564     -323.82196     -8565471.5    
    196000  -324.30158      4038.6851     -323.82196     -5634096.8    
    197000  -324.44261      5226.2386     -323.82196      443851.89    
    198000  -324.53354      5991.9831     -323.82196      5993350.1    
    199000  -324.5697       6296.4193     -323.82196      7393255.8    
    200000  -324.46863      5445.3485     -323.82196      4272906.2    
    200493  -324.39372      4814.6196     -323.82196      1812660.2    
Loop time of 42.6156 on 4 procs for 200000 steps with 101 atoms

Performance: 40548.540 fs/day, 0.001 hours/fs, 4693.118 timesteps/s, 474.005 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.576     | 22.615     | 40.956     | 235.7 | 53.07
Neigh   | 1.9114e-05 | 2.3629e-05 | 2.5892e-05 |   0.0 |  0.00
Comm    | 0.99241    | 19.433     | 30.581     | 255.9 | 45.60
Output  | 0.03344    | 0.035732   | 0.037864   |   0.8 |  0.08
Modify  | 0.066393   | 0.082377   | 0.09318    |   3.4 |  0.19
Other   |            | 0.4486     |            |       |  1.05

Nlocal:          25.25 ave          31 max          21 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost:          75.75 ave          80 max          70 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs:         1262.5 ave        2143 max         476 min
Histogram: 1 0 1 0 0 0 1 0 0 1

Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 2
Dangerous builds = 0

unfix		1
undump		1
undump		2

Total wall time: 0:00:43
